The report was generated using the JSEQ_scRNAseq single-cell analysis pipeline. For more information, please visit: https://github.com/jkubis96/JSEQ_scRNAseq

1 Analysis Configuration Parameters


Parameter	Value
mt_per	25
scale_factor	1e+06
n_features	1500
c_res	0.5
heterogeneity	var
mt_cssg	FALSE
m_val	0.05
top_m	50
max_genes	1000
max_combine	1000
loss_val	0.05
s_factor	0.7
p_bin	0.1
drop	TRUE
min_c	10

The parameters above were used during the current analysis.
If you need to apply different analysis conditions, modify the parameters in the configuration file.

Parameters description:

mt_per
Maximum percentage of mitochondrial genes per cell.
Default: 25%
down
Lower threshold for the number of genes per cell.
Default: NA (automatically computed if NA)
up
Upper threshold for the number of genes per cell.
Default: NA (automatically computed if NA)
scale_factor
Scale factor used for data normalization.
n_features
Number of variable features to detect for clustering.
c_res
Clustering resolution — higher values produce more clusters.
heterogeneity
Method for estimating cluster heterogeneity.
Options: var (within-cluster variance), deg (deregulated gene profiles).
Default: deg
mt_cssg
Whether to include mitochondrial genes when creating subclasses and subtypes.
Options: TRUE, FALSE.
Default: FALSE
m_val
Maximum p-value threshold for marker detection in advanced subtype analyses.
Default: 0.05
top_m
Maximum number of top markers used for naming clusters based on effect size metrics.
Default: 50
max_genes
Maximum number of input genes considered in cluster heterogeneity discovery.
Default: 1000
max_combine
Maximum number of initial combinations for each iteration during heterogeneity discovery.
Default: 1000
loss_val
Assigned value for potentially unclassified cells within a cluster.
s_factor
Maximum split factor for gene occurrence in heterogeneity discovery (0.2–1).
Default: 0.8
p_bin
Minimum cell proportion required for population presence based on binomial test p-value.
Default: 0.05
min_c
Minimum cell proportion required for population presence as defined by the user (independent of binomial test).
Default: 10
drop
Boolean indicating whether to drop non-significant subtypes based on p_bin and min_c.
Default: TRUE

The configuration file is available in the directory:
JSEQ_scRNAseq/requirements_file/config_file.conf

Additional configuration files for other analysis steps can also be found in:
JSEQ_scRNAseq/requirements_file

For more information, please visit:
https://github.com/jkubis96/JSEQ_scRNAseq

2 Cell content analysis

2.1 Read distribution across genomic features

2.2 Count (UMI) per barcode (cell)

2.3 Cell barcode knee plot

The above graph illustrates general trends and quality metrics at the initial stage of single-cell analysis; however, it does not represent the final number of detected cells.

2.4 Ratio of number of genes to counts

2.5 Number of genes and counts per cell

2.6 Percentage of ribosomal and mitochondrial genes [%]

3 Quality control of cell content

3.1 Genes per cell content & thresholds

3.2 Genes upper & lower thresholds per cell

3.3 Number of cells across different stages of analysis

4 Gene expression analysis across cells

4.1 Top highly variable genes in the dataset

5 Princilpe component selection

5.1 ElbowPlot - principal components cutoff

5.2 JackStrawPlot - PC significance

6 Cells clustering

6.1 UMAP clusters

7 Subclasses identification based on marker genes

7.1 PCA cisualization of subclasses

7.2 UMAP visualization of subclasses

7.3 Subclasses - cell composition

7.4 Subclasses markers - top 25

Top 25 merkers
genes	pct_occurrence	esm	avg_logFC	p_val	cluster	p_adj_bf	p_adj_bh	subclass
4930556G01Rik	1.0000000	23.9022539	9.0758183	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Gm18985	0.9090909	19.4858205	9.3266475	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Scn1a	1.0000000	15.4411637	7.8446669	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Rassf6	0.9090909	14.9803329	8.3302664	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Gm33594	0.8181818	14.2863110	9.0676220	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Zfp536.var2	0.9090909	12.6603477	7.7250367	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Col6a4	0.7272727	11.6750888	8.9683165	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Gm29865	0.8181818	10.4756566	7.5963412	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Sugct.var1	0.9090909	9.4800931	6.6899761	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Ido2	0.8181818	9.2158400	7.1815790	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Dgki.var1	0.9090909	8.8739807	6.5749948	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Gm40375	0.7272727	8.4841704	7.1540302	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Slc17a9	0.9090909	8.1299958	6.2600975	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Lipn	0.5454545	8.0562988	8.5338397	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Sorcs1	0.7272727	8.0411011	7.0347095	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Gm20756	0.4545455	7.4214580	9.9622194	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Sh3gl2	0.9090909	6.7189661	5.7612065	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Nfix	1.0000000	6.7182054	5.5549652	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Capn13	0.6363636	6.6828143	6.7673361	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Pde6a	0.7272727	6.6751268	6.2724389	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Rassf2	0.6363636	6.5007340	6.7292426	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Gabra6	0.4545455	6.3123897	7.9380461	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Cnga3	0.3636364	6.0791823	9.6751983	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Wnt2	0.3636364	6.0608144	9.6655899	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Fam71e2	0.4545455	5.7305394	7.2610908	0.0000000	3	0.0000000	0.0000000	CTX Foxg1 4930556g01rik
Gm32067	0.4329897	1.4624655	3.2320719	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Olfr1109	0.2680412	1.2139578	3.7965818	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Rnf19a	0.2577320	1.2121344	3.9703453	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Cux2	0.2371134	1.1630586	4.0620642	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Cdk8	0.4845361	1.1451771	2.3341793	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Trdmt1	0.7525773	1.1326122	1.5858954	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
4931429P17Rik	0.2474227	1.1189843	3.7018578	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Pvr	0.2783505	1.1128852	3.3605800	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Dip2b	0.6288660	1.1067802	1.8467036	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Usp54	0.2886598	1.0937916	3.1370970	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Marchf1	0.3505155	1.0874551	2.7302633	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Cdh13.var1	0.3608247	1.0255035	2.5468172	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Tor3a	0.3814433	1.0120809	2.4285635	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
AW554918	0.2680412	1.0030658	3.0478810	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Scnn1g	0.3711340	1.0019978	2.4250469	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Onecut2	0.4020619	0.9832870	2.2215553	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Gm48228	0.5051546	0.9485065	1.8396507	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Csnk1g1	0.2371134	0.9473673	3.0758585	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
D630023O14Rik	0.1134021	0.9208238	5.6636055	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Fmnl2	0.4432990	0.9207342	1.9597661	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Atp1b2	0.1855670	0.9205405	3.5640036	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Gclc	0.3298969	0.9200055	2.4051085	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Ccdc60	0.2680412	0.9147939	2.6516617	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Aldh1a2	0.1855670	0.9137609	3.5466750	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Gabrd	0.1340206	0.8887066	4.3375463	0.0000000	1	0.0000000	0.0000000	CTX Foxg1 Cdh23.var1
Gm10718	0.7234043	5.3702037	6.9472319	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10801	0.9148936	5.0866180	4.9421851	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10722	0.7659574	5.0746500	6.0229419	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10717	0.5744681	3.8380865	6.3015372	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10800	0.8936170	3.8273154	4.0969425	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm33838	0.5957447	3.6538981	5.6838918	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm11168	0.3191489	2.5918347	7.4491283	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10719	0.3617021	2.4969814	5.7171414	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10721	0.2765957	2.2367176	6.5193877	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10715	0.0851064	1.0918795	5.7071864	0.0000000	2	0.0000000	0.0000000	CTX Foxg1 Gm10801
Gm10720	0.0851064	0.9613444	4.7774679	0.0000000	2	0.0000002	0.0000000	CTX Foxg1 Gm10801
Rwdd3	0.0638298	0.9299216	5.4278515	0.0000000	2	0.0000030	0.0000002	CTX Foxg1 Gm10801
Ss18	0.0851064	0.7871291	3.7039905	0.0000020	2	0.0004383	0.0000337	CTX Foxg1 Gm10801
Abl2	0.0851064	0.7475406	3.4661175	0.0000082	2	0.0018139	0.0001296	CTX Foxg1 Gm10801
Zfp462	0.1276596	0.6555763	2.4786531	0.0000891	2	0.0197795	0.0011635	CTX Foxg1 Gm10801
Gm45740	0.0638298	0.6364140	3.4835747	0.0000597	2	0.0132469	0.0008731	CTX Foxg1 Gm10801
Ddx50	0.0638298	0.6188590	3.3201446	0.0002451	2	0.0544063	0.0027622	CTX Foxg1 Gm10801
Slc6a6	0.0638298	0.6167544	3.4162328	0.0000629	2	0.0139693	0.0008731	CTX Foxg1 Gm10801
Dnajc1	0.0638298	0.6046450	3.2547652	0.0002377	2	0.0527649	0.0027622	CTX Foxg1 Gm10801
Twf1	0.0638298	0.5731906	2.9640853	0.0016644	2	0.3695076	0.0153961	CTX Foxg1 Gm10801
Fam189a1	0.0638298	0.5548877	3.1123516	0.0002489	2	0.0552448	0.0027622	CTX Foxg1 Gm10801
Runx1t1	0.0638298	0.5376714	2.9328344	0.0007283	2	0.1616819	0.0076991	CTX Foxg1 Gm10801
Litaf	0.0638298	0.5208872	2.8796742	0.0007788	2	0.1728844	0.0078460	CTX Foxg1 Gm10801
Dcun1d1	0.0638298	0.5018005	2.6696390	0.0036561	2	0.8116467	0.0253957	CTX Foxg1 Gm10801
Ccser1.var1	0.1063830	0.4956600	2.1767906	0.0008129	2	0.1804591	0.0078460	CTX Foxg1 Gm10801
mt-Rnr2	0.8819562	0.3448005	0.2047558	0.0000000	0	0.0000000	0.0000000	CTX Foxg1 Mt-rnr2
Trim30a	0.4873524	0.0288394	0.0430229	0.0378094	0	0.7561883	0.3780942	CTX Foxg1 Mt-rnr2

7.5 Heatmap of cell subclasses - log(CPM + 1)

7.6 Heatmap of cell subclasses - scale(log(CPM + 1))

8 Subtypes identification based on CSSG genes

8.1 UMAP visualization

8.2 Subtypes - cell composition

8.3 Subtypes markers - top 25

Top 25 markers
genes	pct_occurrence	esm	avg_logFC	p_val	subtype	p_adj_bf	p_adj_bh	cluster
Adgrl3	1.0000000	2.1759120	2.2703800	0.0000000	CTX Emx1 Mt-rnr2 - Adgrl3	0.0000000	0.0000000	0
Gm32067	0.6274510	2.4062788	3.8623922	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Dip2b	1.0000000	2.2154857	2.5036859	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Olfr1109	0.4117647	1.8675132	4.0979103	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Marchf1	0.5098039	1.7056346	3.1833069	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Prune2	0.2941176	1.6273738	4.5361811	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Cux2	0.2941176	1.5625361	4.3228766	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Tor3a	0.5294118	1.5181786	2.8672930	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Usp54	0.3725490	1.5081065	3.4820401	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
4931429P17Rik	0.3137255	1.5033152	3.9944412	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
D630023O14Rik	0.1764706	1.4126324	5.9645874	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Onecut2	0.5294118	1.3876064	2.5421324	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Arhgap31	0.3137255	1.3634223	3.5483788	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Rnf19a	0.2941176	1.3562895	3.6327735	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Cdk8	0.5294118	1.3482082	2.4884015	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Gabrd	0.2156863	1.3215989	4.3948169	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Csnk1g1	0.3137255	1.3180396	3.4232340	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Efhd1	0.1764706	1.3050869	5.1644702	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Gm34719	0.1764706	1.2983052	5.1314056	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Cbr3	0.1960784	1.2894168	4.7085943	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
4930556M19Rik	0.1960784	1.2857535	4.7012500	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Gm12679	0.2549020	1.2749375	3.8274563	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Flt3	0.1568627	1.2612213	5.6081273	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Arhgap18	0.2549020	1.2571639	3.7240657	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Sh3yl1	0.3137255	1.2517741	3.2391273	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Trdmt1	0.7843137	1.2356213	1.6695128	0.0000000	CTX Foxg1 Cdh23.var1 - Dip2b	0.0000000	0.0000000	1
Faf1.var1	0.2941176	3.3114895	7.1077690	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Nfib.var1	1.0000000	2.2962135	2.7406478	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Pik3ca	0.1764706	2.2856142	6.2190926	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
B3gnt5	0.1176471	2.1125210	7.3708281	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Degs1	0.1176471	2.1125074	7.2185105	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Gdap1	0.1176471	2.1125074	7.2185105	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Gt(ROSA)26Sor	0.1176471	2.1125074	7.2185105	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Mvd	0.1176471	2.1125074	7.2185105	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Pdss1	0.1176471	2.1125074	7.2185105	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Shisa2	0.1176471	2.1125074	7.2185105	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Zfp408	0.1176471	2.1125074	7.2185105	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Ikbip	0.1176471	2.1124118	7.6612103	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Nmd3	0.1176471	2.1119719	7.2543696	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Scand1	0.1176471	2.1119719	7.2543696	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Tram1l1	0.1176471	2.1119719	7.2543696	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Katnbl1	0.1176471	2.1118822	7.4042283	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Lifr	0.1176471	2.1117856	7.2496474	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Snrnp48	0.1176471	2.1117856	7.2496474	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Umps	0.1176471	2.1117856	7.2496474	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Fancc	0.1176471	2.1114406	7.3284956	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Abcb8	0.1176471	2.1099555	7.4476811	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Gm12350	0.1176471	2.1093709	7.2989000	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Saal1	0.1176471	2.1089459	7.2943215	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Gfm2	0.1176471	2.1060564	7.3330042	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Colgalt1	0.1176471	2.1053257	7.3296478	0.0000000	CTX Foxg1 Cdh23.var1 - Nfib.var1	0.0000000	0.0000000	1
Gm10718	0.9200000	10.3449031	7.3900604	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm33838	1.0000000	9.1280116	6.2640899	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm10722	0.8800000	6.7628829	6.0734526	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm10717	0.7200000	6.1195030	6.9894671	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm10801	0.9600000	5.2812824	4.8093790	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm11168	0.4400000	4.2254017	9.6988161	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm10719	0.5200000	4.0843766	6.4873682	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm10800	0.9200000	3.9127525	4.0320202	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Gm10721	0.3600000	3.3642292	7.4793644	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000000	0.0000000	2
Dnajc1	0.1200000	1.3679911	5.0199700	0.0000000	CTX Foxg1 Gm10801 - Gm33838	0.0000001	0.0000000	2
Grb2	0.1200000	1.0001602	3.7176376	0.0000036	CTX Foxg1 Gm10801 - Gm33838	0.0002037	0.0000185	2
Ints13	0.1200000	0.8543048	3.2304585	0.0000613	CTX Foxg1 Gm10801 - Gm33838	0.0034343	0.0002862	2
Gpm6b	0.1600000	0.6691492	2.1688539	0.0034731	CTX Foxg1 Gm10801 - Gm33838	0.1944955	0.0149612	2
Rufy3	0.1200000	0.6554352	2.4723140	0.0038493	CTX Foxg1 Gm10801 - Gm33838	0.2155588	0.0153971	2
Ttc28.var1	0.1200000	0.6306612	2.3438878	0.0079540	CTX Foxg1 Gm10801 - Gm33838	0.4454260	0.0247459	2
Zfp462	0.1200000	0.6304118	2.3829412	0.0057779	CTX Foxg1 Gm10801 - Gm33838	0.3235650	0.0212900	2
Dmtn	0.1200000	0.6111338	2.2961561	0.0079059	CTX Foxg1 Gm10801 - Gm33838	0.4427307	0.0247459	2
Ccser1.var1	0.1200000	0.5976588	2.3037403	0.0060829	CTX Foxg1 Gm10801 - Gm33838	0.3406403	0.0212900	2
Macf1	0.1200000	0.5797563	2.1947250	0.0121516	CTX Foxg1 Gm10801 - Gm33838	0.6804900	0.0358153	2
Chd4	0.1600000	0.5056084	1.7260832	0.0167051	CTX Foxg1 Gm10801 - Gm33838	0.9354833	0.0466305	2
Cdc42bpa	0.1200000	0.5003598	1.9688777	0.0174864	CTX Foxg1 Gm10801 - Gm33838	0.9792409	0.0466305	2
Large1.var1	0.1200000	0.4405302	1.7196767	0.0437463	CTX Foxg1 Gm10801 - Gm33838	1.0000000	0.1113541	2
Trim30a	1.0000000	2.2325071	1.9633145	0.0000000	CTX Foxg1 Mt-rnr2 - Trim30a	0.0000000	0.0000000	0
Fabp7	0.1628959	0.2948929	1.1627236	0.0009637	CTX Foxg1 Mt-rnr2 - Trim30a	0.0905872	0.0406421	0
Cdk4	0.1176471	0.2741735	1.3221302	0.0021618	CTX Foxg1 Mt-rnr2 - Trim30a	0.2032105	0.0406421	0
Afm	0.1900452	0.2719298	0.9529706	0.0020540	CTX Foxg1 Mt-rnr2 - Trim30a	0.1930730	0.0406421	0
Hnrnpa2b1	0.2624434	0.2716742	0.7547639	0.0019845	CTX Foxg1 Mt-rnr2 - Trim30a	0.1865445	0.0406421	0
Rps2	0.1493213	0.2610742	1.0676691	0.0030773	CTX Foxg1 Mt-rnr2 - Trim30a	0.2892638	0.0482106	0
Atp5pb	0.1040724	0.2591536	1.3376355	0.0038747	CTX Foxg1 Mt-rnr2 - Trim30a	0.3642173	0.0489335	0
Cnbp	0.1085973	0.2517574	1.2601624	0.0041645	CTX Foxg1 Mt-rnr2 - Trim30a	0.3914676	0.0489335	0
Ptma	0.3167421	0.2459208	0.5881911	0.0050507	CTX Foxg1 Mt-rnr2 - Trim30a	0.4747642	0.0527516	0
Hsp90ab1	0.2488688	0.2374417	0.6768330	0.0077140	CTX Foxg1 Mt-rnr2 - Trim30a	0.7251153	0.0725115	0
Foxg1	0.1176471	0.2315929	1.0639234	0.0107295	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.0840481	0
Rplp0	0.1583710	0.2263801	0.8707091	0.0088856	CTX Foxg1 Mt-rnr2 - Trim30a	0.8352508	0.0759319	0
Rps15a	0.1312217	0.2245464	0.9671396	0.0119566	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.0859406	0
Rpl19	0.1085973	0.2191339	1.0573490	0.0157673	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.0988085	0
mt-Nd2	0.1855204	0.2180027	0.7482510	0.0127997	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.0859406	0
Rpl18a	0.2036199	0.2055220	0.6555629	0.0200491	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1108908	0
H2az1	0.1131222	0.2033407	0.9456098	0.0224556	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1108908	0
Grm8.var1	0.1900452	0.2030050	0.6737175	0.0220805	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1108908	0
Tuba1a	0.3574661	0.2029167	0.4331069	0.0235938	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1108908	0
Rpsa	0.1855204	0.2001264	0.6732538	0.0233572	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1108908	0
Eef1a1	0.2262443	0.1961794	0.5787683	0.0296120	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1185075	0
Tlk1	0.1176471	0.1945612	0.8755234	0.0257185	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1151207	0
Rps21	0.1176471	0.1922929	0.8663250	0.0328908	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1185075	0
Pkm	0.1085973	0.1915755	0.9028033	0.0332047	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1185075	0
Rpl7	0.1628959	0.1894044	0.6976822	0.0293199	CTX Foxg1 Mt-rnr2 - Trim30a	1.0000000	0.1185075	0
Psmc2	1.0000000	2.3943113	2.5631470	0.0000000	CTX Tbr1 Mt-rnr2 - Psmc2	0.0000000	0.0000000	0
Tmeff1	0.1111111	0.9591044	3.8229860	0.0000017	CTX Tbr1 Mt-rnr2 - Psmc2	0.0000576	0.0000288	0
Casp3	0.1111111	0.6713362	2.7744410	0.0002352	CTX Tbr1 Mt-rnr2 - Psmc2	0.0079975	0.0026658	0
Crmp1	0.1111111	0.5032146	2.0116047	0.0117167	CTX Tbr1 Mt-rnr2 - Psmc2	0.3983689	0.0995922	0
Fbxo17	0.1111111	0.3988742	1.6290507	0.0351709	CTX Tbr1 Mt-rnr2 - Psmc2	1.0000000	0.1993017	0
Cdh23.var1	0.8888889	0.2968211	0.2084660	0.0250235	CTX Tbr1 Mt-rnr2 - Psmc2	0.8507984	0.1701597	0
Actb	1.0000000	2.7367861	2.8337028	0.0000000	HIP Lhx2 Mt-rnr2 - Actb	0.0000000	0.0000000	0
Gm35769	0.2666667	0.8998376	2.4290080	0.0000000	HIP Lhx2 Mt-rnr2 - Actb	0.0000001	0.0000000	0
Calu	0.1166667	0.6764668	3.0351923	0.0000011	HIP Lhx2 Mt-rnr2 - Actb	0.0000710	0.0000237	0
Rpl28	0.2000000	0.6520709	2.0697418	0.0000076	HIP Lhx2 Mt-rnr2 - Actb	0.0004728	0.0001182	0
Ndufa4	0.1333333	0.5425358	2.2237514	0.0000640	HIP Lhx2 Mt-rnr2 - Actb	0.0039667	0.0007933	0
Slc25a4	0.1666667	0.3908672	1.3349424	0.0069692	HIP Lhx2 Mt-rnr2 - Actb	0.4320883	0.0720147	0
Trir	0.1166667	0.3446610	1.4415171	0.0179158	HIP Lhx2 Mt-rnr2 - Actb	1.0000000	0.1586831	0
Map1b	0.1833333	0.2887209	0.9237075	0.0450162	HIP Lhx2 Mt-rnr2 - Actb	1.0000000	0.3214989	0
H3f3a	0.2000000	0.2767060	0.8488499	0.0466692	HIP Lhx2 Mt-rnr2 - Actb	1.0000000	0.3214989	0
Cracd	1.0000000	4.3413964	4.1335799	0.0000000	HIP Lhx2 Mt-rnr2 - Cracd	0.0000000	0.0000000	0
Tox4	0.1428571	1.4968645	4.5800441	0.0000001	HIP Lhx2 Mt-rnr2 - Cracd	0.0000060	0.0000030	0
Mgat5b	0.1428571	1.3409596	4.0688387	0.0000064	HIP Lhx2 Mt-rnr2 - Cracd	0.0006948	0.0001507	0
Prdx5	0.1428571	1.3278173	4.0581379	0.0000069	HIP Lhx2 Mt-rnr2 - Cracd	0.0007534	0.0001507	0
Fat4	0.1428571	1.2843780	3.9871693	0.0000066	HIP Lhx2 Mt-rnr2 - Cracd	0.0007235	0.0001507	0
Cotl1	0.1428571	1.2492148	3.8385490	0.0000316	HIP Lhx2 Mt-rnr2 - Cracd	0.0034487	0.0005748	0
Rpl13	0.3571429	1.1645345	2.4332021	0.0000435	HIP Lhx2 Mt-rnr2 - Cracd	0.0047409	0.0006773	0
Sh3bp5	0.1428571	1.1530322	3.5200547	0.0002418	HIP Lhx2 Mt-rnr2 - Cracd	0.0263534	0.0027486	0
Dtnb	0.4285714	1.0976542	2.1132699	0.0000653	HIP Lhx2 Mt-rnr2 - Cracd	0.0071185	0.0008898	0
Eef1g	0.2857143	1.0718869	2.4659255	0.0002805	HIP Lhx2 Mt-rnr2 - Cracd	0.0305781	0.0027486	0
Gm4366	0.1428571	1.0697561	3.3255728	0.0005367	HIP Lhx2 Mt-rnr2 - Cracd	0.0585000	0.0045000	0
Snx10	0.1428571	1.0530481	3.3737997	0.0002902	HIP Lhx2 Mt-rnr2 - Cracd	0.0316315	0.0027486	0
St18	0.1428571	1.0515638	3.3733466	0.0003026	HIP Lhx2 Mt-rnr2 - Cracd	0.0329829	0.0027486	0
Hsd17b12	0.1428571	0.9801404	3.1303315	0.0011759	HIP Lhx2 Mt-rnr2 - Cracd	0.1281701	0.0085447	0
Pitpnb	0.1428571	0.9604932	3.0931674	0.0011489	HIP Lhx2 Mt-rnr2 - Cracd	0.1252307	0.0085447	0
Psme3	0.1428571	0.9405393	3.0119448	0.0020125	HIP Lhx2 Mt-rnr2 - Cracd	0.2193584	0.0121866	0
Smc1a	0.1428571	0.9337071	2.9489503	0.0031978	HIP Lhx2 Mt-rnr2 - Cracd	0.3485556	0.0183450	0
Wnk1	0.1428571	0.9139764	2.9649732	0.0019699	HIP Lhx2 Mt-rnr2 - Cracd	0.2147177	0.0121866	0
Mllt3	0.2142857	0.8616247	2.4110290	0.0020014	HIP Lhx2 Mt-rnr2 - Cracd	0.2181518	0.0121866	0
Ncoa1	0.1428571	0.8613500	2.7505360	0.0071277	HIP Lhx2 Mt-rnr2 - Cracd	0.7769245	0.0356196	0
Ndufa6	0.1428571	0.8301252	2.7769354	0.0038164	HIP Lhx2 Mt-rnr2 - Cracd	0.4159836	0.0207992	0
Elavl3	0.1428571	0.7970417	2.6283762	0.0071893	HIP Lhx2 Mt-rnr2 - Cracd	0.7836318	0.0356196	0
Epha4	0.1428571	0.7849074	2.5750942	0.0101405	HIP Lhx2 Mt-rnr2 - Cracd	1.0000000	0.0442126	0
Eif1ax	0.1428571	0.7673469	2.5389928	0.0098189	HIP Lhx2 Mt-rnr2 - Cracd	1.0000000	0.0442126	0
Rpl7-ps7	0.1428571	0.7481943	2.5108011	0.0109859	HIP Lhx2 Mt-rnr2 - Cracd	1.0000000	0.0450627	0
Zfp263	1.0000000	2.4900947	2.6600593	0.0000000	HIP Lhx2 Mt-rnr2 - Zfp263	0.0000000	0.0000000	0
Gnai3	0.1041667	0.5885046	2.5767424	0.0003847	HIP Lhx2 Mt-rnr2 - Zfp263	0.0192342	0.0064114	0
Gm15500	0.1458333	0.5766988	2.1370966	0.0002662	HIP Lhx2 Mt-rnr2 - Zfp263	0.0133100	0.0064114	0
Pcgf5	0.1458333	0.4378360	1.5770827	0.0076492	HIP Lhx2 Mt-rnr2 - Zfp263	0.3824615	0.0956154	0
Rpl5-ps1	0.1041667	0.4010093	1.7544370	0.0125557	HIP Lhx2 Mt-rnr2 - Zfp263	0.6277859	0.1255572	0
Cse1l	0.1041667	0.3837506	1.6259381	0.0260587	HIP Lhx2 Mt-rnr2 - Zfp263	1.0000000	0.1924005	0
Grtp1	0.1041667	0.3784897	1.6101445	0.0269361	HIP Lhx2 Mt-rnr2 - Zfp263	1.0000000	0.1924005	0
Trpc4	0.1458333	0.3288938	1.1717066	0.0429275	HIP Lhx2 Mt-rnr2 - Zfp263	1.0000000	0.2384863	0
mt-Rnr2	0.8750000	0.1029803	0.0581472	0.0414073	HIP Lhx2 Mt-rnr2 - Zfp263	1.0000000	0.2384863	0
Cdh13.var1	1.0000000	3.6957805	3.7254609	0.0000000	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000000	0.0000000	0
Sphk2	0.1666667	3.0794291	8.3593756	0.0000000	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000000	0.0000000	0
Stard9	0.1666667	3.0765997	8.3426832	0.0000000	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000000	0.0000000	0
Fbp2	0.1666667	2.3024650	6.0459530	0.0000000	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000000	0.0000000	0
Hsd17b4	0.2500000	1.9064409	4.2189546	0.0000000	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000002	0.0000000	0
Cdk14	0.1666667	1.7239751	4.5941767	0.0000001	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000047	0.0000007	0
Ank2.var1	0.2500000	1.7150628	3.9661696	0.0000000	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000014	0.0000002	0
Serinc3	0.1666667	1.5175461	4.2132863	0.0000009	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000574	0.0000067	0
Zfp428	0.1666667	1.4901004	4.1769103	0.0000009	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0000602	0.0000067	0
Lrrc4c	0.1666667	1.4416775	4.0195542	0.0000048	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0003069	0.0000307	0
Macroh2a2	0.1666667	1.4391829	3.9179379	0.0000191	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0012243	0.0001113	0
Gbf1	0.1666667	1.2496869	3.5934047	0.0000582	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0037230	0.0003103	0
Gdpd1	0.1666667	1.2373176	3.5147601	0.0001541	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0098609	0.0007585	0
Erh	0.1666667	1.1045866	3.2160514	0.0006449	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0412723	0.0027515	0
Kansl1	0.1666667	1.0874738	3.2440992	0.0003576	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0228865	0.0016348	0
Snrpg	0.1666667	1.0624357	3.0985526	0.0009991	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0639401	0.0037612	0
Top1	0.3333333	1.0466885	2.2428058	0.0007492	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0479482	0.0029968	0
Mycn	0.1666667	1.0080408	3.0194711	0.0010843	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.0693956	0.0038553	0
6030443J06Rik	0.1666667	0.9580883	2.9033824	0.0020708	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.1325327	0.0064477	0
Midn	0.1666667	0.9494962	2.8900923	0.0019001	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.1216075	0.0064004	0
Atp5o.var2	0.1666667	0.9377545	2.7900429	0.0039749	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.2543955	0.0110607	0
Psmd13	0.1666667	0.9369532	2.8782068	0.0022555	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.1443514	0.0065614	0
Tcerg1	0.1666667	0.8915705	2.8001041	0.0021156	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.1354011	0.0064477	0
Mllt11	0.1666667	0.8743143	2.6545727	0.0054677	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.3499320	0.0145805	0
Id2	0.1666667	0.8251033	2.4787674	0.0127966	STR Foxp1 Mt-rnr2 - Cdh13.var1	0.8189822	0.0327593	0
Dynll2	1.0000000	6.2715042	5.1554995	0.0000000	STR Foxp1 Mt-rnr2 - Dynll2	0.0000000	0.0000000	0
Gm6540	0.1538462	2.8194794	8.2402049	0.0000000	STR Foxp1 Mt-rnr2 - Dynll2	0.0000000	0.0000000	0
Ccnd2	0.6153846	2.3188025	3.2267531	0.0000000	STR Foxp1 Mt-rnr2 - Dynll2	0.0000000	0.0000000	0
Impdh2	0.1538462	1.8060374	5.1547612	0.0000000	STR Foxp1 Mt-rnr2 - Dynll2	0.0000000	0.0000000	0
Wipi1	0.1538462	1.6317788	4.4023342	0.0000023	STR Foxp1 Mt-rnr2 - Dynll2	0.0002393	0.0000356	0
Ndel1	0.1538462	1.4778308	4.2034406	0.0000023	STR Foxp1 Mt-rnr2 - Dynll2	0.0002393	0.0000356	0
Pqbp1	0.1538462	1.4612217	4.1836529	0.0000025	STR Foxp1 Mt-rnr2 - Dynll2	0.0002613	0.0000356	0
Setd2	0.1538462	1.3528421	4.0494816	0.0000027	STR Foxp1 Mt-rnr2 - Dynll2	0.0002852	0.0000356	0
Gm13456	0.1538462	1.3212397	3.8023041	0.0000429	STR Foxp1 Mt-rnr2 - Dynll2	0.0045512	0.0004199	0
Cdc123	0.1538462	1.2610491	3.7182546	0.0000460	STR Foxp1 Mt-rnr2 - Dynll2	0.0048708	0.0004199	0
Cyb5r3	0.1538462	1.2473821	3.6317722	0.0001251	STR Foxp1 Mt-rnr2 - Dynll2	0.0132605	0.0010066	0
Arhgap11a	0.1538462	1.2375468	3.6935636	0.0000475	STR Foxp1 Mt-rnr2 - Dynll2	0.0050385	0.0004199	0
Cenpb	0.1538462	1.2097038	3.5748355	0.0001329	STR Foxp1 Mt-rnr2 - Dynll2	0.0140919	0.0010066	0
Dars	0.1538462	1.1098694	3.3602734	0.0003183	STR Foxp1 Mt-rnr2 - Dynll2	0.0337427	0.0021089	0
Tpt1	0.6153846	1.1056760	1.6863578	0.0000465	STR Foxp1 Mt-rnr2 - Dynll2	0.0049334	0.0004199	0
Ccdc50	0.1538462	1.0916855	3.2771433	0.0006612	STR Foxp1 Mt-rnr2 - Dynll2	0.0700822	0.0031856	0
Pdhb	0.1538462	1.0772720	3.2549052	0.0006448	STR Foxp1 Mt-rnr2 - Dynll2	0.0683459	0.0031856	0
Trappc1	0.1538462	1.0633134	3.2352592	0.0006209	STR Foxp1 Mt-rnr2 - Dynll2	0.0658161	0.0031856	0
Rpl14-ps1	0.1538462	1.0534183	3.2175263	0.0006612	STR Foxp1 Mt-rnr2 - Dynll2	0.0700822	0.0031856	0
Smyd3.var1	0.1538462	1.0517621	3.2765585	0.0003183	STR Foxp1 Mt-rnr2 - Dynll2	0.0337427	0.0021089	0
Senp5	0.1538462	1.0508760	3.1572843	0.0011218	STR Foxp1 Mt-rnr2 - Dynll2	0.1189138	0.0051702	0
Rpl18	0.2307692	1.0255263	2.7079740	0.0004202	STR Foxp1 Mt-rnr2 - Dynll2	0.0445391	0.0026199	0
mt-Co1	0.4615385	1.0062840	1.8883374	0.0004602	STR Foxp1 Mt-rnr2 - Dynll2	0.0487816	0.0027101	0
Tm2d1	0.1538462	0.9925999	3.0164391	0.0018875	STR Foxp1 Mt-rnr2 - Dynll2	0.2000740	0.0083364	0
Mki67	0.1538462	0.9895409	3.0174655	0.0019702	STR Foxp1 Mt-rnr2 - Dynll2	0.2088392	0.0083536	0

8.4 Heatmap of cell subtypes - log(CPM + 1)

8.5 Heatmap of cell subtypes - scale(log(CPM + 1))

9 Disclaimer

The analysis was performed through the non-profit and open-source pipeline JSEQ_scRNAseq. Remember, in silico analysis must be validated in vitro or in vivo. For more information, visit GitHub or contact us. JSEQ_scRNAseq was created at the Institute of Bioorganic Chemistry, Polish Academy of Sciences.

JSEQ_scRNAseq - REPORT

2025-11-27